30 Aug
2023
30 Aug
'23
8:42 a.m.
Dear all,
I have installed nestml via conda and developed a code describing an LIF
neuron with bi-exponential synaptic currents including NMDA, while the
charge mediated by AMPA and NMDA receptors are not independent. When I try
to compile the .nestml file, it gives me an error as:
from pynestml.frontend.pynestml_frontend import generate_nest_target
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
In [2]:
generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml",
...: target_path="/tmp/nestml-component",
...: logging_level="ERROR")
line 61:4 extraneous input 'end' expecting {DEDENT, 'function',
'state',
'parameters', 'internals', 'update', 'equations',
'input', 'output'}
line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
...
r"""Generate and build code for NEST Simulator.
Parameters
A dictionary containing additional options for the target code generator.
"""
I was wondering what the reason could be. I would appreciate it if you
could help.
Thanks in advance.
Best,
Hedyeh
30 Aug
30 Aug
9:47 a.m.
Dear Hedyeh,
the |end| keyword has recently been removed from NESTML. You indicate
blocks now solely by indentation as in Python.
Cheers,
Jochen!
On 30.08.23 08:42, Hedyeh Rezaei wrote:
Dear all,
I have installed nestml via conda and developed a code describing an
LIF neuron with bi-exponential synaptic currents including NMDA, while
the charge mediated by AMPA and NMDA receptors are not independent.
When I try to compile the .nestml file, it gives me an error as:
from pynestml.frontend.pynestml_frontend import generate_nest_target
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
In [2]:
generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml",
...: target_path="/tmp/nestml-component",
...: logging_level="ERROR")
line 61:4 extraneous input 'end' expecting {DEDENT, 'function',
'state', 'parameters', 'internals', 'update',
'equations', 'input',
'output'}
line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
...
r"""Generate and build code for NEST Simulator.
Parameters
A dictionary containing additional options for the target code generator.
"""
I was wondering what the reason could be. I would appreciate it if you
could help.
Thanks in advance.
Best,
Hedyeh
_______________________________________________
NEST Users mailing list --users(a)nest-simulator.org
To unsubscribe send an email tousers-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
10:51 a.m.
Dear Jochen,
Thanks a lot, a giant step forward!
I now get another error:
Variable 'g_ex' not defined!
Ode equation lhs-variable 'g_ex$' not defined in state block!
Ode equation lhs-variable 'g_in$' not defined in state block!
Ode equation lhs-variable 'g_NMDA$' not defined in state block!
...
AttributeError: 'NoneType' object has no attribute 'is_state'
While my state block contains:
state:
r integer = 0 # counts number of tick during the
refractory period
V_m mV = E_L # membrane potential
# inputs from the inhibitory conductance
g_in real = 0
g_in$ real = g_I_const * (1 / tau_rise_GABA_A - 1 /
tau_decay_GABA_A)
# inputs from the excitatory conductance
g_ex real = 0
g_ex$ real = g_E_const * (1 / tau_rise_AMPA - 1 / tau_decay_AMPA)
# inputs from the excitatory NMDA conductance
g_NMDA real = 0
g_NMDA$ real = g_NMDA_const * (1 / tau_rise_NMDA - 1 /
tau_decay_NMDA)
Any suggestions?
Thanks,
Hedyeh
On Wed, Aug 30, 2023 at 9:47 AM Jochen Martin Eppler <j.eppler(a)fz-juelich.de>
wrote:
Dear Hedyeh,
the end keyword has recently been removed from NESTML. You indicate
blocks now solely by indentation as in Python.
Cheers,
Jochen!
On 30.08.23 08:42, Hedyeh Rezaei wrote:
Dear all,
I have installed nestml via conda and developed a code describing an LIF
neuron with bi-exponential synaptic currents including NMDA, while the
charge mediated by AMPA and NMDA receptors are not independent. When I try
to compile the .nestml file, it gives me an error as:
from pynestml.frontend.pynestml_frontend import generate_nest_target
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
In [2]:
generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml",
...: target_path="/tmp/nestml-component",
...: logging_level="ERROR")
line 61:4 extraneous input 'end' expecting {DEDENT, 'function',
'state',
'parameters', 'internals', 'update', 'equations',
'input', 'output'}
line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
...
r"""Generate and build code for NEST Simulator.
Parameters
A dictionary containing additional options for the target code generator.
"""
I was wondering what the reason could be. I would appreciate it if you
could help.
Thanks in advance.
Best,
Hedyeh
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
10:52 a.m.
Dear Hedyeh,
Could you post the complete .nestml file (on the list or to me directly if you prefer) so
we can try to reproduce the issue?
Much obliged!
Charl
On Wed, Aug 30, 2023, at 10:51, Hedyeh Rezaei wrote:
Dear Jochen,
Thanks a lot, a giant step forward!
I now get another error:
Variable 'g_ex' not defined!
Ode equation lhs-variable 'g_ex$' not defined in state block!
Ode equation lhs-variable 'g_in$' not defined in state block!
Ode equation lhs-variable 'g_NMDA$' not defined in state block!
...
AttributeError: 'NoneType' object has no attribute 'is_state'
While my state block contains:
state:
r integer = 0 # counts number of tick during the refractory period
V_m mV = E_L # membrane potential
# inputs from the inhibitory conductance
g_in real = 0
g_in$ real = g_I_const * (1 / tau_rise_GABA_A - 1 / tau_decay_GABA_A)
# inputs from the excitatory conductance
g_ex real = 0
g_ex$ real = g_E_const * (1 / tau_rise_AMPA - 1 / tau_decay_AMPA)
# inputs from the excitatory NMDA conductance
g_NMDA real = 0
g_NMDA$ real = g_NMDA_const * (1 / tau_rise_NMDA - 1 / tau_decay_NMDA)
Any suggestions?
Thanks,
Hedyeh
On Wed, Aug 30, 2023 at 9:47 AM Jochen Martin Eppler <j.eppler(a)fz-juelich.de>
wrote:
Dear Hedyeh,
the `end` keyword has recently been removed from NESTML. You indicate blocks now solely
by indentation as in Python.
Cheers,
Jochen!
On 30.08.23 08:42, Hedyeh Rezaei wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
Dear all,
I have installed nestml via conda and developed a code describing an LIF neuron with
bi-exponential synaptic currents including NMDA, while the charge mediated by AMPA and
NMDA receptors are not independent. When I try to compile the .nestml file, it gives me an
error as:
from pynestml.frontend.pynestml_frontend import generate_nest_target
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
In [2]:
generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml",
...: target_path="/tmp/nestml-component",
...: logging_level="ERROR")
line 61:4 extraneous input 'end' expecting {DEDENT, 'function',
'state', 'parameters', 'internals', 'update',
'equations', 'input', 'output'}
line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
...
r"""Generate and build code for NEST Simulator.
Parameters
A dictionary containing additional options for the target code generator.
"""
I was wondering what the reason could be. I would appreciate it if you could help.
Thanks in advance.
Best,
Hedyeh
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
1 Sep
1 Sep
3:04 p.m.
Dear Charl,
I sent my .nestml file to your email address.
I would be grateful if you could help.
Looking forward to hearing from you.
Best regards,
Hedyeh
On Wed, Aug 30, 2023 at 10:53 AM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Dear Hedyeh,
Could you post the complete .nestml file (on the list or to me directly if
you prefer) so we can try to reproduce the issue?
Much obliged!
Charl
On Wed, Aug 30, 2023, at 10:51, Hedyeh Rezaei wrote:
Dear Jochen,
Thanks a lot, a giant step forward!
I now get another error:
Variable 'g_ex' not defined!
Ode equation lhs-variable 'g_ex$' not defined in state block!
Ode equation lhs-variable 'g_in$' not defined in state block!
Ode equation lhs-variable 'g_NMDA$' not defined in state block!
...
AttributeError: 'NoneType' object has no attribute 'is_state'
While my state block contains:
state:
r integer = 0 # counts number of tick during the
refractory period
V_m mV = E_L # membrane potential
# inputs from the inhibitory conductance
g_in real = 0
g_in$ real = g_I_const * (1 / tau_rise_GABA_A - 1 /
tau_decay_GABA_A)
# inputs from the excitatory conductance
g_ex real = 0
g_ex$ real = g_E_const * (1 / tau_rise_AMPA - 1 / tau_decay_AMPA)
# inputs from the excitatory NMDA conductance
g_NMDA real = 0
g_NMDA$ real = g_NMDA_const * (1 / tau_rise_NMDA - 1 /
tau_decay_NMDA)
Any suggestions?
Thanks,
Hedyeh
On Wed, Aug 30, 2023 at 9:47 AM Jochen Martin Eppler <
j.eppler(a)fz-juelich.de> wrote:
Dear Hedyeh,
the end keyword has recently been removed from NESTML. You indicate
blocks now solely by indentation as in Python.
Cheers,
Jochen!
On 30.08.23 08:42, Hedyeh Rezaei wrote:
Dear all,
I have installed nestml via conda and developed a code describing an LIF
neuron with bi-exponential synaptic currents including NMDA, while the
charge mediated by AMPA and NMDA receptors are not independent. When I try
to compile the .nestml file, it gives me an error as:
from pynestml.frontend.pynestml_frontend import generate_nest_target
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
In [2]:
generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml",
...: target_path="/tmp/nestml-component",
...: logging_level="ERROR")
line 61:4 extraneous input 'end' expecting {DEDENT, 'function',
'state',
'parameters', 'internals', 'update', 'equations',
'input', 'output'}
line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
...
r"""Generate and build code for NEST Simulator.
Parameters
A dictionary containing additional options for the target code generator.
"""
I was wondering what the reason could be. I would appreciate it if you
could help.
Thanks in advance.
Best,
Hedyeh
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
251
days inactive
253
days old
4 comments
3 participants
participants (3)
-
Charl Linssen -
Hedyeh Rezaei -
Jochen Martin Eppler